To re-produce the issue is quite easy:

1. Create a workflow job with Definition Workflow script from SCM (with for example git@bitbucket.org:<ACCOUNT>/git-bitbucket.git) and then you specify a script Path flow-ci-dev.groovy with:

node {
    stage 'checkout'
    git credentialsId: '', url: 'git@bitbucket.org:<ACCOUNT>/git-bitbucket.git'
}

2. Click to build the job

You will see duplicated changes like the ones attached.

Not sure if this is a duplicate of JENKINS-29326 or if the issue is in Workflow or the git-plugin directly.